.TH g_sgangle 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_sgangle - computes the angle and distance between two groups

.B VERSION 4.5
.SH SYNOPSIS
\f3g_sgangle\fP
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-s" " topol.tpr "
.BI "\-oa" " sg_angle.xvg "
.BI "\-od" " sg_dist.xvg "
.BI "\-od1" " sg_dist1.xvg "
.BI "\-od2" " sg_dist2.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]one" ""
.BI "\-[no]z" ""
.SH DESCRIPTION
\&Compute the angle and distance between two groups. 
\&The groups are defined by a number of atoms given in an index file and
\&may be two or three atoms in size.
\&If \-one is set, only one group should be specified in the index
\&file and the angle between this group at time 0 and t will be computed.
\&The angles calculated depend on the order in which the atoms are 
\&given. Giving for instance 5 6 will rotate the vector 5\-6 with 
\&180 degrees compared to giving 6 5. 

If three atoms are given, 
\&the normal on the plane spanned by those three atoms will be
\&calculated, using the formula  P1P2 x P1P3.
\&The cos of the angle is calculated, using the inproduct of the two
\&normalized vectors.


\&Here is what some of the file options do:

\&\-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.

\&\-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.

\&\-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.

\&\-od2: For two planes this option has no meaning.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input
 Index file 

.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-oa" " sg_angle.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-od" " sg_dist.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-od1" " sg_dist1.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-od2" " sg_dist2.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]one"  "no    "
 Only one group compute angle between vector at time zero and time t

.BI "\-[no]z"  "no    "
 Use the Z\-axis as reference

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
